The ninja tool ignores content signatures generated by subst expansions. Normally this is not a problem because most subst expansions don't produce a different content signature from their own expansion, but in some cases (like SERVER-49299) the user will provide an alternate content signature from the expansion. 

This means ninja will incorrectly not rebuild certain items because it lacks information regarding a subst expansion. Possibly ninja could re-perform the subst expansion for signature checking to determine if it needs to rebuild by extracting the python code in some form and running it in a scons context. It would be hard.